GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Methylocapsa aurea KYG

Align BadH (characterized)
to candidate WP_036258924.1 DL86_RS05195 acetoacetyl-CoA reductase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_000746085.1:WP_036258924.1
          Length = 241

 Score =  143 bits (360), Expect = 4e-39
 Identities = 90/247 (36%), Positives = 130/247 (52%), Gaps = 9/247 (3%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66
           + AV++GG  GIG A  +     G K+A      D  E  A    + G      + D+++
Sbjct: 3   RVAVVSGGSRGIGAAISKGLHAAGYKVAATYAGND--EAAANFKAETG--IPVYKWDVSN 58

Query: 67  RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126
                  +      LGP++IL+NNAG      F K  P +W  +I  NL    +M   V+
Sbjct: 59  YKECAEGLKKVGDDLGPIEILINNAGITRDTMFHKMTPEQWFDVINTNLNSLFNMTRPVI 118

Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186
            GM ER  GRIVNI+S   + G  G+  Y A K G + F+K+LA+E+A  GITVN VCPG
Sbjct: 119 EGMRERGFGRIVNISSINGQKGQMGQTNYTASKAGDIGFTKSLAQENAGKGITVNAVCPG 178

Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246
              T ++      A   E L ++    IPL RLG+P+++A  + F  ++++GFITG  LS
Sbjct: 179 YIATDMVK-----AVPKEVLEKSVLPLIPLRRLGEPEEVARVVVFLVAEESGFITGSTLS 233

Query: 247 VSGGLTM 253
           V+GG  M
Sbjct: 234 VNGGQYM 240


Lambda     K      H
   0.318    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 155
Number of extensions: 3
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 241
Length adjustment: 24
Effective length of query: 231
Effective length of database: 217
Effective search space:    50127
Effective search space used:    50127
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory